Non-Cooperative Interactions Between Transcription Factors and Clustered DNA Binding Sites Enable Graded Transcriptional Responses To Environmental Inputs

Abstract

A paradigm in transcriptional regulation is that graded increases in transcription factor (TF) concentrations are translated into digital on/off transcriptional responses by cooperative TF binding to adjacent cognate sites. Such digital transcriptional responses underlie the definition of anatomical boundaries during development. Here we show that NF-kB, a key TF controlling inflammation and immunity, is conversely an analog transcriptional regulator relying on the non-cooperative usage of clustered homotypic sites. Contrary to the paradigm, we observed that increasing concentrations of NF-kB are translated into gradual increments in transcription of target genes. We provide a thermodynamic interpretation of the experimental observations by combining quantitative measurements and a minimal physical model of an NF-kB-dependent promoter. We demonstrate that NF-kB binds independently to adjacent sites to promote additive RNA-Pol II recruitment and graded transcriptional outputs. These findings reveal a novel paradigm in the usage of clustered TF binding sites, which may be extensively applied to the biological conditions in which the transcriptional output is proportional to the strength of an environmental input.